The pizza chain La Porchetta will self-audit employees' pay at a third of its outlets after two Melbourne franchises were found to have underpaid some of their workers.

La Porchetta has agreed with the Fair Work Ombudsman to a three-year self-audit of wages at 24 of its 65 stores after the Federal Court found that 111 employees, mostly teenagers, including one aged 13, had been underpaid a total of $258,000 at franchises in Pakenham and Berwick between 2009 and 2012.

The companies that run the two restaurants – Bound for Glory Enterprises Pty Ltd and Zillion Zenith International Pty Ltd – were each fined $139,507.50 in the Federal Court earlier this month. The owner of both companies, Ruby Chand, was fined a further $55,803.

The companies will repay more than $79,000 in wages not already reimbursed to workers.

The audit will involve permanent and casual staff, and La Porchetta Franchising has agreed to work with franchisees to ensure prompt repayment where irregularities are found, the Fair Work Ombudsman, Natalie James, said.

New franchisees will get induction training and receive employment packs with information about employment laws. All employees will be given annual refresher training.

James said she was pleased with La Porchetta Franchising's positive approach in entering a proactive compliance deed with her office to investigate wage problems and resolve them.

“This deed is an example of how the Fair Work Ombudsman continues to look for ways to assist employers and employees to be able to put good practices in place that can assist people to resolve issues in the workplace themselves,” she said.

"Employers who care about their reputation should be doing these sorts of things."